SNP calling exercise answers part 2 - Revision history

Mick at 13:24, 7 January 2026

2026-01-07T13:24:01Z

← Older revision		Revision as of 15:24, 7 January 2026
Line 6:		Line 6:

	<pre>		<pre>
	gatk VariantFiltration \		/home/ctools/gatk-4.6.2.0/gatk VariantFiltration \
	-V NA24694.vcf.gz \		-V NA24694.vcf.gz \
	-O NA24694_hf.vcf.gz \		-O NA24694_hf.vcf.gz \
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	<pre>		<pre>
	bcftools view -H NA24694_hf.vcf.gz \| grep -v PASS \| wc -l		/home/ctools/bcftools-1.23/bcftools view -H NA24694_hf.vcf.gz \| grep -v PASS \| wc -l
	</pre>		</pre>

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	<pre>		<pre>
	bcftools view -H --type=snps NA24694_hf.vcf.gz \| grep -v PASS \| wc -l		/home/ctools/bcftools-1.23/bcftools view -H --type=snps NA24694_hf.vcf.gz \| grep -v PASS \| wc -l
	</pre>		</pre>

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	<pre>		<pre>
	bcftools view -H NA24694_hf.vcf.gz \		/home/ctools/bcftools-1.23/bcftools view -H NA24694_hf.vcf.gz \
	\| grep -v PASS \		\| grep -v PASS \
	\| cut -f7 \		\| cut -f7 \
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	<pre>		<pre>
	bcftools view -f PASS NA24694_hf.vcf.gz \		/home/ctools/bcftools-1.23/bcftools view -f PASS NA24694_hf.vcf.gz \
	\| bgzip -c > NA24694_hf_pass.vcf.gz		\| /home/ctools/htslib-1.20/bgzip -c > NA24694_hf_pass.vcf.gz
	</pre>		</pre>

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	<pre>		<pre>
	bcftools view -H NA24694_hf_pass.vcf.gz \| wc -l		/home/ctools/bcftools-1.23/bcftools view -H NA24694_hf_pass.vcf.gz \| wc -l
	</pre>		</pre>

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	-a NA24694_hf_pass.vcf.gz \		-a NA24694_hf_pass.vcf.gz \
	-b /home/databases/databases/GRCh38/filter99.bed.gz \		-b /home/databases/databases/GRCh38/filter99.bed.gz \
	\| bgzip -c > NA24694_hf_map99.vcf.gz		\| /home/ctools/htslib-1.20/bgzip -c > NA24694_hf_map99.vcf.gz
	</pre>		</pre>

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	<pre>		<pre>
	bcftools view -H NA24694_hf_map99.vcf.gz \| wc -l		/home/ctools/bcftools-1.23/bcftools view -H NA24694_hf_map99.vcf.gz \| wc -l
	</pre>		</pre>

Line 110:		Line 110:
	GRCh38.99 \		GRCh38.99 \
	NA24694_hf.vcf.gz \		NA24694_hf.vcf.gz \
	\| bgzip -c > NA24694_hf_ann.vcf.gz		\| /home/ctools/htslib-1.20/bgzip -c > NA24694_hf_ann.vcf.gz
	</pre>		</pre>

Mick at 09:15, 26 November 2025

2025-11-26T09:15:50Z

Show changes

Gabre: Created page with " '''Q1''' First running:

 gatk VariantFiltration     -V NA24694.vcf.gz  -O NA24694_hf.vcf.gz   -filter "DP < 10.0" --filter-name "DP"    -filter "QUAL < 30.0" --filter-name "QUAL30"     -filter "SOR > 3.0" --filter-name "SOR3"     -filter "FS > 60.0" --filter-name "FS60"     -filter "MQ < 40.0" --filter-name "MQ40"

and

  bcftools view  -H NA24694_hf.vcf.gz |grep -v PASS |wc -l

Gives us 4005 sites.

  bcftools view  -H  --type=..."

2025-01-08T12:26:42Z

Created page with " '''Q1''' First running: <pre> gatk VariantFiltration -V NA24694.vcf.gz -O NA24694_hf.vcf.gz -filter "DP < 10.0" --filter-name "DP" -filter "QUAL < 30.0" --filter-name "QUAL30" -filter "SOR > 3.0" --filter-name "SOR3" -filter "FS > 60.0" --filter-name "FS60" -filter "MQ < 40.0" --filter-name "MQ40" </pre> and <pre> bcftools view -H NA24694_hf.vcf.gz |grep -v PASS |wc -l </pre> Gives us 4005 sites. <pre> bcftools view -H --type=..."

New page

'''Q1'''

First running:

<pre>
gatk VariantFiltration -V NA24694.vcf.gz -O NA24694_hf.vcf.gz -filter "DP < 10.0" --filter-name "DP" -filter "QUAL < 30.0" --filter-name "QUAL30" -filter "SOR > 3.0" --filter-name "SOR3" -filter "FS > 60.0" --filter-name "FS60" -filter "MQ < 40.0" --filter-name "MQ40"

</pre>

and

<pre>
bcftools view -H NA24694_hf.vcf.gz |grep -v PASS |wc -l
</pre>

Gives us 4005 sites.

<pre>
bcftools view -H --type=snps NA24694_hf.vcf.gz |grep -v PASS |wc -l
</pre>
2630 SNPs

'''Q2'''

One possibility is:
<pre>
bcftools view -H NA24694_hf.vcf.gz |grep -v PASS |cut -f 7 |sort |uniq -c |sort -n
5 FS60;SOR3
30 DP;MQ40;SOR3
74 MQ40;SOR3
158 DP;SOR3
197 DP;MQ40
390 MQ40
1340 SOR3
1811 DP
</pre>

This says remove all lines with the string "PASS", extract the seventh column, sort them, unique and count them, sort again but according to numerical order. At the bottom, you have the most used filter which is depth of coverage.

'''Q3'''

Initially, we isolate the ones that pass the filter:
<pre>
bcftools view -f PASS NA24694_hf.vcf.gz |bgzip -c > NA24694_hf_pass.vcf.gz
bcftools view -H NA24694_hf_pass.vcf.gz |wc -l
</pre>
88594 total sites (SNPS+indels+multi-allelic).

Then we retain the sites using bedtools:
<pre>
bedtools intersect -header -a NA24694_hf_pass.vcf.gz -b /home/databases/databases/GRCh38/filter99.bed.gz |bgzip -c > NA24694_hf_map99.vcf.gz
</pre>

<pre>
bcftools view -H NA24694_hf_map99.vcf.gz |wc -l
</pre>
51624 total sites remain

'''Q4'''
Using:
<pre>
java -jar /home/ctools/snpEff/snpEff.jar eff -dataDir /home/databases/databases/snpEff/ -htmlStats NA24694_hf.html GRCh38.99 NA24694_hf.vcf.gz |bgzip -c > NA24694_hf_ann.vcf.gz
</pre>

In the HTML file you see:
Intron 64.368%

'''Q5'''
In the HTML file you see:

MISSENSE 584 44.242%

So a total of 584 detecting mutations can have an impact on the protein sequence.